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- PDB-6y34: Streptavidin wildtype with a biotC5-1 cofactor - an artificial ir... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y34 | ||||||||||||||||||
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Title | Streptavidin wildtype with a biotC5-1 cofactor - an artificial iron hydroxylase | ||||||||||||||||||
![]() | Streptavidin | ||||||||||||||||||
![]() | OXIDOREDUCTASE / Artificial Metalloenzyme / Iron Hydroxylase / Biotin-Binding Protein | ||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Serrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / Ward, T.R. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Enantioselective Hydroxylation of Benzylic C(sp3)-H Bonds by an Artificial Iron Hydroxylase Based on the Biotin-Streptavidin Technology. Authors: Serrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / Ward, T.R. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6y25C ![]() 6y2mC ![]() 6y2tC ![]() 6y33C ![]() 6y3qC ![]() 3pk2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16569.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P22629 |
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#2: Chemical | ChemComp-O7Q / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.307→45.998 Å / Num. obs: 38242 / % possible obs: 99.3 % / Redundancy: 25.4 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.307→1.33 Å / Redundancy: 22.9 % / Rmerge(I) obs: 2.702 / Num. unique obs: 1785 / CC1/2: 0.552 / % possible all: 95.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3PK2 Resolution: 1.307→45.998 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.178 / Average fsc free: 0.912 / Average fsc work: 0.9175 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.046 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.282 Å2
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Refinement step | Cycle: LAST / Resolution: 1.307→45.998 Å
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Refine LS restraints |
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LS refinement shell |
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